[Bioperl-l] CVS AND PAML

Luba Pardo lubapardo at gmail.com
Tue Apr 17 05:16:04 EDT 2007


Dear all,
I have two questions.
1.) I am trying to download some modules from Bioperl-run via CVS but I can
not login.

$ cvs -d :pserver:cvs at code.open-bio.org:/home/repository/bioperl login.

The error I get is: time out, failed to connect to the server. I have
no trouble to download other files and I installed bioperl modules via
CPAN and it works.

2) The second question I have is that I am using the PAML:CODEML
module to do phylogenetic analysis.

I have used the example provided in the HOWTO:PAML (also given as
example: pairwise_ka_ks.PL). The program does not crash but it returns
and empty object. I think the problem is in the last part of the
script because I manage to get sequences and also the alignment, but I
can not get any ka, ks value. I am not sure whether there is a bug in
the last part of the script.

Does anyone have an idea?

Thank you very much

Luba Pardo

$kaks_factory->alignment($dna_aln);

# run the KaKs analysis
my ($rc,$parser) = $kaks_factory->run();
my $result = $parser->next_result;
my $MLmatrix = $result->get_MLmatrix();

my @otus = $result->get_seqs();
# this gives us a mapping from the PAML order of sequences back to
# the input order (since names get truncated)
my @pos = map <http://www.perldoc.com/perl5.6/pod/func/map.html> {
    my $c= 1;
    foreach my $s ( @each ) {
      last if( $s->display_id eq $_->display_id );
      $c++;
    }
    $c;
   } @otus;

print <http://www.perldoc.com/perl5.6/pod/func/print.html> OUT join
<http://www.perldoc.com/perl5.6/pod/func/join.html>("\t", qw
<http://www.perldoc.com/perl5.6/pod/func/qw.html>(SEQ1 SEQ2 Ka Ks
Ka/Ks PROT_PERCENTID CDNA_PERCENTID)),"\n";
for( my $i = 0; $i < (scalar
<http://www.perldoc.com/perl5.6/pod/func/scalar.html> @otus -1) ;
$i++) {
  for( my $j = $i+1; $j < (scalar
<http://www.perldoc.com/perl5.6/pod/func/scalar.html> @otus); $j++ ) {
    my $sub_aa_aln  = $aa_aln->select_noncont($pos[$i],$pos[$j]);
    my $sub_dna_aln = $dna_aln->select_noncont($pos[$i],$pos[$j]);
    print <http://www.perldoc.com/perl5.6/pod/func/print.html> OUT
join <http://www.perldoc.com/perl5.6/pod/func/join.html>("\t",
$otus[$i]->display_id,
                         $otus[$j]->display_id,$MLmatrix->[$i]->[$j]->{'dN'},
                         $MLmatrix->[$i]->[$j]->{'dS'},
                         $MLmatrix->[$i]->[$j]->{'omega'},
                         sprintf
<http://www.perldoc.com/perl5.6/pod/func/sprintf.html>("%.2f",$sub_aa_aln->percentage_identity),
                         sprintf
<http://www.perldoc.com/perl5.6/pod/func/sprintf.html>("%.2f",$sub_dna_aln->percentage_identity),
                         ), "\n";
  }
}


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